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SYA_PYRHO_1_752

Alanine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family]

Composition of the binding site

Protein chains monomer
A1 (SYA_PYRHO):99, 128, 140:142, 145, 147, 192, 210:213, 215, 248:250, 252, 25599, 128, 140:142, 145, 147, 192, 210:213, 215, 248:250, 252, 255
Metals (Me):Zn

Full PDB list

2zze, 2zzf, 2zzg (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
A
9
9
R
1
2
8
R
1
4
0
H
1
4
1
F
1
4
2
F
1
4
5
M
1
4
7
W
1
9
2
E
2
1
0
V
2
1
1
A
2
1
2
T
2
1
3
V
2
1
5
D
2
4
8
T
2
4
9
G
2
5
0
G
2
5
2
R
2
5
5
[1]2zze.a none . . . . . . . . . . . . . . . . . . Zn
[1]2zzg.a a5a28 . . . . . . . . . . . . . . . . . . Zn

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

[download in TSV format]
   
PDB.ch
A1 Me
A
9
9
R
1
2
8
R
1
4
0
H
1
4
1
F
1
4
2
F
1
4
5
M
1
4
7
W
1
9
2
E
2
1
0
V
2
1
1
A
2
1
2
T
2
1
3
V
2
1
5
D
2
4
8
T
2
4
9
G
2
5
0
G
2
5
2
R
2
5
5
[1]2zze.a . . . . . . . . . . . . . . . . . . Zn
[1]2zzg.a . . . . . . . . . . . . . . . . . . Zn

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
2zze.a is apo
2zzg.a:a5a
[1] 2zze.a
-
0.3
[1] 2zzg.a -
0.1
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
2zze.a
2zzg.a
[1] 2zze.a
0
.01
[1] 2zzg.a .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
2zze.a
2zzg.a
[1] 2zze.a
0
0.7
[1] 2zzg.a 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
2zze.a
2zzg.a
[1] 2zze.a
0
1.6
[1] 2zzg.a 1.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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